diff --git a/html/cgi-bin/ids.cgi b/html/cgi-bin/ids.cgi
index bb124bdfe..76848f71a 100644
--- a/html/cgi-bin/ids.cgi
+++ b/html/cgi-bin/ids.cgi
@@ -141,11 +141,12 @@ if ($cgiparams{'RULESET'} eq $Lang::tr{'update'}) {
 	my $enabled_sids_file = "$IDS::settingsdir/oinkmaster-enabled-sids.conf";
 	my $disabled_sids_file = "$IDS::settingsdir/oinkmaster-disabled-sids.conf";
 
-	# Arrays to store sid which should be added to the corresponding files.
-	my @enabled_sids;
-	my @disabled_sids;
+	# Arrays to store which rulefiles have been enabled and will be used.
 	my @enabled_rulefiles;
 
+	# Hash to store the user-enabled and disabled sids.
+	my %enabled_disabled_sids;
+
 	# Loop through the hash of idsrules.
 	foreach my $rulefile(keys %idsrules) {
 		# Check if the rulefile is enabled.
@@ -158,6 +159,13 @@ if ($cgiparams{'RULESET'} eq $Lang::tr{'update'}) {
 		}
 	}
 
+	# Read-in the files for enabled/disabled sids.
+	# This will be done by calling the read_enabled_disabled_sids_file function two times
+	# and merge the returned hashes together into the enabled_disabled_sids hash.
+	%enabled_disabled_sids = (
+		&read_enabled_disabled_sids_file($disabled_sids_file),
+		&read_enabled_disabled_sids_file($enabled_sids_file));
+
 	# Loop through the hash of idsrules.
 	foreach my $rulefile (keys %idsrules) {
 		# Loop through the single rules of the rulefile.
@@ -171,8 +179,8 @@ if ($cgiparams{'RULESET'} eq $Lang::tr{'update'}) {
 				if ($idsrules{$rulefile}{$sid}{'State'} eq "off") {
 					# Check if the state has been set to 'on'.
 					if ($cgiparams{$sid} eq "on") {
-						# Add the sid to the enabled_sids array.
-						push(@enabled_sids, $sid);
+						# Add/Modify the sid to/in the enabled_disabled_sids hash.
+						$enabled_disabled_sids{$sid} = "enabled";
 
 						# Drop item from cgiparams hash.
 						delete $cgiparams{$rulefile}{$sid};
@@ -184,8 +192,8 @@ if ($cgiparams{'RULESET'} eq $Lang::tr{'update'}) {
 					# Check if the state is 'on' and should be disabled.
 					# In this case there is no entry
 					# for the sid in the cgiparams hash.
-					# Add it to the disabled_sids array.
-					push(@disabled_sids, $sid);
+					# Add/Modify it to/in the enabled_disabled_sids hash.
+					$enabled_disabled_sids{$sid} = "disabled";
 
 					# Drop item from cgiparams hash.
 					delete $cgiparams{$rulefile}{$sid};
@@ -195,38 +203,39 @@ if ($cgiparams{'RULESET'} eq $Lang::tr{'update'}) {
 	}
 
 	# Open enabled sid's file for writing.
-	open(FILE, ">$enabled_sids_file") or die "Could not write to $enabled_sids_file. $!\n";
-
-	# Write header to file.
-	print FILE "#Autogenerated file. Any custom changes will be overwritten!\n";
-
-	# Check if the enabled_sids array contains any sid's.
-	if (@enabled_sids) {
-		# Loop through the array of enabled sids and write them to the file.
-		foreach my $sid (@enabled_sids) {
-			print FILE "enablesid $sid\n";
-		}
-	}
-
-	# Close file after writing.
-	close(FILE);
+	open(ENABLED_FILE, ">$enabled_sids_file") or die "Could not write to $enabled_sids_file. $!\n";
 
 	# Open disabled sid's file for writing.
-	open(FILE, ">$disabled_sids_file") or die "Could not write to $disabled_sids_file. $!\n";
+	open(DISABLED_FILE, ">$disabled_sids_file") or die "Could not write to $disabled_sids_file. $!\n";
 
-	# Write header to file.
-	print FILE "#Autogenerated file. Any custom changes will be overwritten!\n";
+	# Write header to the files.
+	print ENABLED_FILE "#Autogenerated file. Any custom changes will be overwritten!\n";
+	print DISABLED_FILE "#Autogenerated file. Any custom changes will be overwritten!\n";
 
-	# Check if the enabled_sids array contains any sid's.
-        if (@disabled_sids) {
-		# Loop through the array of disabled sids and write them to the file.
-		foreach my $sid (@disabled_sids) {
-			print FILE "disablesid $sid\n";
+	# Check if the hash for enabled/disabled files contains any entries.
+	if (%enabled_disabled_sids) {
+		# Loop through the hash.
+		foreach my $sid (keys %enabled_disabled_sids) {
+			# Check if the sid is enabled.
+			if ($enabled_disabled_sids{$sid} eq "enabled") {
+				# Print the sid to the enabled_sids file.
+				print ENABLED_FILE "enablesid $sid\n";
+			# Check if the sid is disabled.
+			} elsif ($enabled_disabled_sids{$sid} eq "disabled") {
+				# Print the sid to the disabled_sids file.
+				print DISABLED_FILE "disablesid $sid\n";
+			# Something strange happende - skip the current sid.
+			} else {
+				next;
+			}
 		}
 	}
 
-	# Close file after writing.
-	close(FILE);
+	# Close file for enabled_sids after writing.
+	close(ENABLED_FILE);
+
+	# Close file for disabled_sids after writing.
+	close(DISABLED_FILE);
 
 	# Open file for used rulefiles.
 	open (FILE, ">$idsusedrulefilesfile") or die "Could not write to $idsusedrulefilesfile. $!\n";