The present work aimed to investigate the effect of the harvest time and site of fruit picking at the plant on the health quality of cotton seeds. In laboratory, seeds were submitted to the tests of viability-standard germination and tetrazolium, tests of vigour (tetrazolium and emergency rate in field) and seed health test to detect fungi (?Blotter Test?). The results of seed viability tests showed no statistical difference between the treatments, harvest time and picking site of fruit; however, treating seeds with fungicide increased germination rate. The results of the following vigour tests emergency rate in fieid, revealid statistical differences between the treatments-harvest time and site of fruit picking at the plant. The highest levels of seed vigour were obtained when the harvest was made 2 weeks following the stage in which plants had 50% of the fruits open. Seeds produced at the lower part of the plant, treated witch fungicide, showed higher potential to stablish on initial population of plant. Regarding the seeds health quality the results showed that Colletotrichum gossypii was the most frequent patogen. Fusarium sp occurred also in high frequence in seeds of fruits picked at higher part of the plants. The results of this word showed therefore that harvest time and site of fruit picking at the cotton plants may affect health quality of seeds of cotton.