The reproductive stage in many crops, including maize, is very sensitive to heat stress and the genetic overlap between gametophytic and sporophytic phase gives an opportunity to select superior stress tolerant genotype at gametophytic stage. An attempt was made to evaluate the response of cyclic pollen selection in the F₁ and F₂ generations on the performance of F₃ generation progenies for seed yield and yield contributing traits under natural heat stress conditions. In this direction three groups of F₃ progenies, namely (i) pollen selection in F₁ and F₂ generations (GG), (ii) pollen selection only in F₂ generation (CG), (iii) no pollen selection in F₁ and F₂ generations (CC) were screened for heat stress at Agricultural Research Station (ARS), Bheemarayanagudi. The GG progenies recorded significantly higher chlorophyll content, more number of pollen grains per anther and less pollen sterility compared to CG and CC group of progeniesunder heat stress. Further, the F₄ progenies obtained through cyclic pollen selection (in F₁, F₂ and F₃) were also tested for heat stress tolerance at seedling stage. The significant improvement for heat stress tolerance was recorded in F₄ progenies derived through cyclic pollen selection as compared to control (no pollen selection for heat tolerance in any generation) F₄ progenies. The results indicated that cyclic pollen selection in F₁, F₂ and F₃ generations improved the heat stress tolerance of the progenies in the succeeding generations. To provide genetic evidence for the effect of pollen selection for heat tolerance, the control F₂ (C) and selected F₂ (G) populations were compared for the segregation of SSR markers. The selected F₂ (G) population showed significant deviation from normal Mendelian ratio of 1:2:1 and showed skewness towards the alleles selected from male parent. The results provide strong evidence for an increase in the frequency of parental alleles in the progenies that impart heat stress tolerance.