A study was undertaken at the Teaching and Research farm of the University of Agriculture Makurdi in 2005, 2006 and 2007 to determine the effects of fruit size on the seed quality of ‘egusi-itoo’ melon (Cucumeropsis mannii Naudin). Fruits at maturity were harvested and grouped based on their sizes into big, medium and small categories. Data were collected on fruit length, diameter and weight. In addition, number of seeds per fruit, dry seed weight per fruit and 100-seed weight were also taken. Thereafter, seeds were extracted and tested for viability before and after storage at ambient temperature. Results revealed that seeds extracted from bigger fruits yielded higher values over those from smaller fruits in all the other parameters studied except germination percentage where no significant differences were found among the fruit sizes. Germination of stored seeds from all fruit sizes deteriorated with storage period and completely failed when test was conducted after three years. It was therefore concluded that Cucumeropsis mannii seeds could be extracted from fruits of all sizes without jeopardizing quality.