use strict;
use warnings;

my $s1 = '<citref idrefs="cit">5c,5d,5Es</citref>';
my $s2 = '<qwerty alrefs="xad">5c,5d,5Es</qwerty>';

print parse($s1)."\n";
print parse($s2)."\n";

sub parse {
    my $orig = shift;
    my ($cit, $idrefs, $values, @values);

    $orig    =~ m/.*?>(.*)<\//;
    $values  = $1;
    @values  = split ',', $values;
    $orig    =~ m/.*?"(.*)">/;
    $cit     = $1;
    $idrefs .= "$cit$_ " for @values;
    chop $idrefs;

    $orig =~ s/(.*?=").*(">.*)/$1$idrefs$2/;

    @values = map{ s/([a-z]+)/<it>$1<\/it>/i; $_;} @values;
    $values = join ',', @values;
    $orig   =~ s/>.*?</'>'.$values.'<'/es;

    return $orig;
}
[download]

<citref idrefs="cit5c cit5d cit5Es">5<it>c</it>,5<it>d</it>,5<it>Es</i
+t></citref>
<qwerty alrefs="xad5c xad5d xad5Es">5<it>c</it>,5<it>d</it>,5<it>Es</i
+t></qwerty>
[download]

Hi,

I have tried to produce the exact output of yours with the same input, i got these codes,

use strict;

while(<DATA>){
    chomp;
    $_=~s/(<citref idrefs=\")([^"]*)(\">)((?:(?!<\/citref>).)*)(<\/cit
+ref>)/$1.idgen($2,$4).$3.citeref($4).$5/sgie;    
    print "$_\n";    
}

sub idgen{
    my ($id,$idcon) = @_;    
    if($idcon =~/,/){
        $idcon=~s/([^,]+)(?=,|$)/$id$1/gi;
        $idcon=~s/,/ /gi;
    }
    else{
        $idcon=$id.$idcon;
    }    
    return($idcon);
}

sub citeref{
    my ($con) = @_;
    if($con =~/,/){
        my (@con) = split/,/,$con;        
        map{s/[a-z]+/<it>$&<\/it>/i} @con;
        $con =join(',',@con);
    }
    else{        
        $con =~s/[a-z]+/<it>$&<\/it>/gi;        
    }
    
    return($con);
}
[download]

__DATA__
<citref idrefs="cit">5c,5d</citref>
<citref idrefs="cit">5d</citref>
[download]

But please explain us furthermore to provide you the better solution like,

1. The content of the 'citref' tag (i.e) it will always contain the comma or not

2. The idrefs generated in the output should be preceded with the idref content of input or it will always be 'cit'

Punitha