diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
index 423dc1b23..0b8e23de3 100644
--- a/docs/Doxyfile.in
+++ b/docs/Doxyfile.in
@@ -790,6 +790,8 @@ INPUT = \
     @abs_top_srcdir@/libdispatch/dv2i.c \
     @abs_top_srcdir@/libsrc4/nc4file.c \
     @abs_top_srcdir@/libsrc4/nc4var.c \
+    @abs_top_srcdir@/libsrc4/nc4hdf.c \
+    @abs_top_srcdir@/libsrc4/nc4internal.c \
     @abs_top_srcdir@/examples/C/simple_xy_wr.c \
     @abs_top_srcdir@/examples/C/simple_xy_rd.c \
     @abs_top_srcdir@/examples/C/sfc_pres_temp_wr.c \
diff --git a/libsrc4/nc4hdf.c b/libsrc4/nc4hdf.c
index b15072b67..8bb27f9d9 100644
--- a/libsrc4/nc4hdf.c
+++ b/libsrc4/nc4hdf.c
@@ -1,16 +1,18 @@
-/*
-  This file is part of netcdf-4, a netCDF-like interface for HDF5, or a
-  HDF5 backend for netCDF, depending on your point of view.
-
-  This file contains functions internal to the netcdf4 library. None of
-  the functions in this file are exposed in the exetnal API. These
-  functions handle the HDF interface.
-
-  Copyright 2003, University Corporation for Atmospheric
-  Research. See the COPYRIGHT file for copying and redistribution
-  conditions.
-
-  $Id: nc4hdf.c,v 1.273 2010/05/27 21:34:14 dmh Exp $
+/**
+ *
+ * @file
+ * This file is part of netcdf-4, a netCDF-like interface for HDF5, or a
+ * HDF5 backend for netCDF, depending on your point of view.
+ *
+ * This file contains functions internal to the netcdf4 library. None of
+ * the functions in this file are exposed in the exetnal API. These
+ * functions handle the HDF interface.
+ *
+ * Copyright 2003, University Corporation for Atmospheric
+ * Research. See the COPYRIGHT file for copying and redistribution
+ * conditions.
+ *
+ * @author Ed Hartnett, Dennis Heimbigner, Ward Fisher
 */
 
 #include "config.h"
@@ -535,11 +537,21 @@ set_par_access(NC_HDF5_FILE_INFO_T *h5, NC_VAR_INFO_T *var, hid_t xfer_plistid)
 }
 #endif
 
-/* Write an array of data to a variable. When it comes right down to
- * it, this is what netCDF-4 is all about, this is *the* function, the
- * big enchilda, the grand poo-bah, the alpha dog, the head honcho,
- * the big cheese, the mighty kahuna, the top bananna, the high
- * muckity-muck, numero uno. Well, you get the idea.  */
+/**
+ * @internal Write an array of data to a variable.
+ *
+ * @param nc Pointer to the file NC struct.
+ * @param ncid File ID.
+ * @param varid Variable ID.
+ * @param startp Array of start indicies.
+ * @param countp Array of counts.
+ * @param mem_nc_type The type of the data in memory.
+ * @param is_long True only if NC_LONG is the memory type.
+ * @param data The data to be written.
+ *
+ * @returns NC_NOERR No error.
+ * @author Ed Hartnett
+ */
 int
 nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
              const size_t *countp, nc_type mem_nc_type, int is_long, void *data)
diff --git a/libsrc4/nc4internal.c b/libsrc4/nc4internal.c
index 97351c16c..0919335d3 100644
--- a/libsrc4/nc4internal.c
+++ b/libsrc4/nc4internal.c
@@ -1,16 +1,18 @@
-/** \file \internal
-Internal netcdf-4 functions.
-
-This file contains functions internal to the netcdf4 library. None of
-the functions in this file are exposed in the exetnal API. These
-functions all relate to the manipulation of netcdf-4's in-memory
-buffer of metadata information, i.e. the linked list of NC
-structs.
-
-Copyright 2003-2011, University Corporation for Atmospheric
-Research. See the COPYRIGHT file for copying and redistribution
-conditions.
-
+/**
+ * @file
+ * @internal
+ * Internal netcdf-4 functions.
+ *
+ * This file contains functions internal to the netcdf4 library. None of
+ * the functions in this file are exposed in the exetnal API. These
+ * functions all relate to the manipulation of netcdf-4's in-memory
+ * buffer of metadata information, i.e. the linked list of NC
+ * structs.
+ * 
+ * Copyright 2003-2011, University Corporation for Atmospheric
+ * Research. See the COPYRIGHT file for copying and redistribution
+ * conditions.
+ * @author Ed Hartnett
 */
 #include "config.h"
 #include "nc4internal.h"
@@ -33,7 +35,6 @@ h5catch(void* ignored)
 }
 #endif
 
-
 /* These are the default chunk cache sizes for HDF5 files created or
  * opened with netCDF-4. */
 extern size_t nc4_chunk_cache_size;
@@ -259,6 +260,18 @@ nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grpp, NC_HDF5_FILE_INFO_T **h5p)
     return NC_NOERR;
 }
 
+/**
+ * @internal Find info for this file and group, and set pointer to each. 
+ *
+ * @param ncid File and group ID.
+ * @param nc Pointer that gets a pointer to the file's NC struct.
+ * @param grpp Pointer that gets a pointer to the group struct.
+ * @param h5p Pointer that gets HDF5 file struct.
+ *
+ * @returns NC_NOERR No error.
+ * @returns NC_EBADID Bad ncid.
+ * @author Ed Hartnett 
+*/
 int
 nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grpp,
 		   NC_HDF5_FILE_INFO_T **h5p)
@@ -287,7 +300,15 @@ nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grpp,
     return NC_NOERR;
 }
 
-/* Recursively hunt for a group id. */
+/**
+ * @internal Recursively hunt for a group id. 
+ *
+ * @param start_grp Pointer to group where search should be started.
+ * @param tartget_nc_grpid Group ID to be found.
+ *
+ * @returns Pointer to group info struct, or NULL if not found.
+ * @author Ed Hartnett
+*/
 NC_GRP_INFO_T *
 nc4_rec_find_grp(NC_GRP_INFO_T *start_grp, int target_nc_grpid)
 {
@@ -309,8 +330,18 @@ nc4_rec_find_grp(NC_GRP_INFO_T *start_grp, int target_nc_grpid)
    return NULL;
 }
 
-/* Given an ncid and varid, get pointers to the group and var
- * metadata. */
+/**
+ * @internal Given an ncid and varid, get pointers to the group and var
+ * metadata. 
+ *
+ * @param nc Pointer to file's NC struct.
+ * @param ncid File ID.
+ * @param varid Variable ID.
+ * @param grp Pointer that gets pointer to group info.
+ * @param var Pointer that gets pointer to var info.
+ *
+ * @returns NC_NOERR No error.
+ */
 int
 nc4_find_g_var_nc(NC *nc, int ncid, int varid,
 		  NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var)
@@ -324,7 +355,7 @@ nc4_find_g_var_nc(NC *nc, int ncid, int varid,
    /* It is possible for *grp to be NULL. If it is,
       return an error. */
    if(*grp == NULL)
-     return NC_ENOTVAR;
+     return NC_EBADID;
 
    /* Find the var info. */
    if (varid < 0 || varid >= (*grp)->vars.nelems)
@@ -334,7 +365,18 @@ nc4_find_g_var_nc(NC *nc, int ncid, int varid,
    return NC_NOERR;
 }
 
-/* Find a dim in a grp (or parents). */
+/**
+ * @internal Find a dim in a grp (or its parents). 
+ *
+ * @param grp Pointer to group info struct.
+ * @param dimid Dimension ID to find.
+ * @param dim Pointer that gets pointer to dim info if found.
+ * @param dim_grp Pointer that gets pointer to group info of group that contians dimension. 
+ * 
+ * @returns ::NC_NOERR No error.
+ * @returns ::NC_BADDIM Dimension not found.
+ * @author Ed Hartnett
+ */
 int
 nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim,
 	     NC_GRP_INFO_T **dim_grp)
diff --git a/nc_test4/tst_vars3.c b/nc_test4/tst_vars3.c
index c5f8cc1f3..fd200f16c 100644
--- a/nc_test4/tst_vars3.c
+++ b/nc_test4/tst_vars3.c
@@ -398,8 +398,7 @@ main(int argc, char **argv)
 
       /* Try to write some data, but fail. */
       if (nc_put_vara_double(ncid + MILLION, 0, start, count, double_data) != NC_EBADID) ERR;
-      /* This should return NC_EBADID, but returns NC_ENOTVAR. */
-      if (nc_put_vara_double(ncid + TEST_VAL_42, 0, start, count, double_data) != NC_ENOTVAR) ERR;
+      if (nc_put_vara_double(ncid + TEST_VAL_42, 0, start, count, double_data) != NC_EBADID) ERR;
 
       if (nc_close(ncid)) ERR;
    }