Population viability analysis (PVA) is used in conservation biology to predict extinction probabilities for threatened species. Previous studies have revealed large differences between the predictions of PVA modeling packages, but these comparisons included a range of nonstandard factors. A standardized comparison of five PVA packages (GAPPS, INMAT, RAMAS Metapop, RAMAS Stage, and VORTEX) was conducted on six examples (two mammals, two birds, one reptile, and a hypothetical bird/mammal-like life history). The individual-based packages (GAPPS and VORTEX) predicted a consistently higher risk of extinction than their matrix-based counterparts (INMAT and the RAMAS programs). This arose as only the former considered the effect of demographic stochasticity in the sex ratio. The difference was eliminated when only females were modeled in the matrix-based packages. To avoid underestimating extinction risk, only the limiting sex should be modeled in matrix-based PVA packages.