The absence of juvenile sexual dimorphism in birds often impedes sex determination using external morphology. We examined sex ratio variation in Scopoli's Shearwater (Calonectris diomedea) fledglings (n = 135) on a Strofades island (southern Ionian Sea) between 2007 and 2011. We determined sex by using a polymerase chain reaction-based methodology on blood samples. The molecular technique revealed a slightly male-biased sex ratio (52.6% ) during the five consecutive breeding seasons. In addition, morphological analysis using six morphometric variables (bill length, bill width, nalospi, bill-head length, head length, tarsus length) and body weight indicated that males were significantly larger than females for all the tested variables. The combined use of those variables correctly classified 81.2% of known-sex fledglings, and the stepwise discriminant analysis pointed out that bill length was the most discriminating variable followed by bill depth, head length, and body weight.