Sequence polymorphisms result in phenotypic variation through the pathways of interacting genes and their products. We focused on transcript-level variation in the splicing pathway for sex determination – a model network defining downstream morphological characters that are dimorphic between males and females. Expression of Sex lethal, transformer, transformer2, doublesex, intersex and hermaphrodite was assayed with quantitative RT-PCR in 0- to 1-day-old adult males and females of 36 Drosophila melanogaster inbred lines. Abundant genetic variation in the transcript levels was found for all genes. Sex-specific splices had high concentrations in the appropriate sex. In the other sex, low but detectable concentrations were also observed. Abundances of splices strongly co-varied between sexes among genotypes, with little genetic variation strictly limited to one sex. The level of sexually dimorphic Yolk protein1 expression – an immediate downstream target of the pathway – was modelled as the target phenotype of the upstream sex determination pathway. Substantial genetic variation in this phenotype in males was explained by leaky splicing of female-specific transcripts. If higher transcript levels of the appropriate isoform of sex determination genes are beneficial in a sex, then stronger leakiness of the inappropriate transcript might be deleterious, perhaps contributing to the fitness trade-offs previously observed between the sexes.