This works: 
my %seen;
my @lines;

while (<DATA>) {
    my @cols = split /\s+/;
    unless ($seen{$cols[0]}++) {
        push @lines, $_;
    }
}

print @lines;

__DATA__
XXXXXS331632    XXXXXS331632    female  40087   a5
XXXXXS331632    XXXXXS331632    female  47735   a5
XXXXXS331681    XXXXXS331681    male    40087   e6
XXXXXS331681    XXXXXS331681    male    47735   e6
XXXXXS331856    XXXXXS331856    male    40177   d1
XXXXXS331856    XXXXXS331856    male    47737   d1

[download]
Output: 
$ ./721691.pl
XXXXXS331632    XXXXXS331632    female  40087   a5
XXXXXS331681    XXXXXS331681    male    40087   e6
XXXXXS331856    XXXXXS331856    male    40177   d1

[download]
Edit: Misread the question and used the wrong column for the ID.

In reply to Re: Remove duplicate lines in a file by lostjimmy
in thread Remove duplicate lines in a file by Anonymous Monk

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