In traits suspected to be governed by at least two loci, linkage analysis incorporating the joint action of both loci may improve the power to detect linkage, increase the precision of estimating locus positions and provide insight into the underlying etiological mechanism. Recently, we mapped two susceptibility loci for epilepsy-related photosensitivity (or photoparoxysmal response, PPR) at regions 7q32 (PPR1) and 16p13 (PPR2) in PPR families with prominent myoclonic seizures background (MS-related PPR). To follow-up these results and evaluate interaction effects between these regions, we conducted two-locus (2L) linkage analyses using parametric and non-parametric methods. The 2L linkage was calculated under a multiplicative (MULT) epistasis model, encompassing models where each locus is necessary but not sufficient for MS-related PPR and a heterogeneity (HET) model, encompassing models in which each locus is by itself sufficient but not necessary for MS-related PPR expression. We found maximal 2L linkage under the (MULT) model, which was significantly better than the 2L linkage under the (HET) model (P = 0.001). The 2L analyses gave no increase in power to detect linkage over the single-locus analyses nor did they improve location estimates at PPR1 and PPR2, as expected under a best-fit 2L (MULT) model in an affecteds-only analysis. Our findings suggest that the genes underlying the PPR1 and PPR2 susceptibility loci may have similar functions or act in the same biochemical pathway. Genet. Epidemiol. © 2006 Wiley-Liss, Inc.