There are 84 distinct cultivars of highland bananas (Musa spp.) in Uganda, grouped in five clone sets and it is not known which among these are female fertile. The objective of the study reported herein was to identify female fertile highland bananas that can be used in a cross breeding program and to determine the influence of pistil morphological traits on seed set. Seventy eight cultivars were screened for female fertility using pollen from ‘Calcutta 4\' and thirty-three cultivars representing the major variability of highland bananas were selected for studying pistil morphological traits to establish their relationship with seed yield. The clone sets and cultivars were highly significantly (P