Background: Research on gender differences in intelligence has focused mostly on samples from Western countries and empirical evidence on gender differences from Southeast Asia is relatively sparse. Aims: This article presents results on gender differences in variance and means on a non-verbal intelligence test using a national sample of public school students from the Philippines. Sample: More than 2,700 sixth graders from public schools across the country were tested with the Naglieri Non-verbal Ability Test (NNAT). Methods: Variance ratios (VRs) and log-transformed VRs were computed. Proportion ratios for each of the ability levels were also calculated and a chi-square goodness-of-fit test was performed. An analysis of variance was performed to determine the overall gender difference in mean scores as well as within each of three age subgroups. Results: Our data show non-existent or trivial gender difference in mean scores. However, the tails of the distributions show differences between the males and females, with greater variability among males in the upper half of the distribution and greater variability among females in the lower half of the distribution. Descriptions of the results and their implications are discussed. Conclusions: Results on mean score differences support the hypothesis that there are no significant gender differences in cognitive ability. The unusual results regarding differences in variance and the male-female proportion in the tails require more complex investigations.