BACKGROUND: Recent attention has been paid to patterns of fluctuating asymmetry (FA) in paired bilateral traits and the extent to which they reflect phenotypic and genetic quality. The FA-fertility hypothesis proposes that FA may be a reliable indicator of ejaculate quality in humans and other animals. The common control by the Hox genes of the differentiation of both the urogenital system and the appendicular skeleton in vertebrates has been proposed as an explanation for the recent finding that FA, and the second to fourth digit ratios (2D:4D) are both associated with semen quality in men. METHODS: A group of 50 men was evaluated for FA, calculated by the sum of three different body FAs, 2D:4D ratios, and seminal parameters of masturbatory semen samples. RESULTS: Composite FA had a significant effect on semen parameters; the 2D:4D ratios did not predict semen quality. CONCLUSIONS: Comparison of our data with previous studies suggests that the putative relationship between semen quality and 2D:4D may have been driven by the inclusion of severely oligozoospermic men within the original subject group. Our sample included men with equally high 2D:4D ratios but who had normal semen. Thus, the 2D:4D ratio may not reliably indicate poor semen quality although FA might.