A key question for molecular and behavioural ecologists who study mating systems is to understand why, in many species, females choose to mate with extra-pair males. Recently a possible explanation, ‘genetic compatibility’, has gained increasing empirical support (for a comprehensive review, see Kempenaers 2007). Genetic compatibility hypotheses assume that females seek extra-pair mates with alleles that complement their own. Typically, this will be achieved by mating with a male of a different genotype than her own, in order to maximise the heterozygosity of her offspring. Because numerous studies have indicated positive associations between heterozygosity and fitness (see Coltman & Slate 2003), it follows that mating with ‘compatible’ males will result in heterozygous, and therefore fit, offspring. Most empirical support for genetic compatibility has been obtained with microsatellite markers that have first been used to assess parentage and then to estimate relatedness and/or individual heterozygosity. A problem with this approach is a possible bias that favours the detection of extra-pair paternity when the extra-pair male has a genotype different from that of the female and her social mate. This in turn could lead to the erroneous conclusion that extra-pair males are less related to the female than within-pair males. In this issue of Molecular Ecology, Wetzel & Westneat 2009 (hereafter W&W), use simulation studies to assess the extent of this bias, using parameter estimates obtained from recent empirical data. They identify two forms of bias that may affect tests of the genetic compatibility hypothesis, and provide guidelines on how these biases may be avoided.