Unpollinated flower culture was applied for induction of gynogenesis and somatic organogenesis in three shallot strains, ‘Dili-white’, ‘Yogya’ and ‘Dili-red’, from Indonesia. Chromosome surveys were performed on the plants obtained. From a total of 6,812 flowers, 89 plantlets were obtained by gynogenesis, of which 10 could be acclimated. Most of the plantlets were induced from ‘Dili-white’. Of the gynogenetic plants examined, two were haploid (2n = 8), four were naturally doubled haploid (2n = 16) and the remaining four were mixoploid (2n = 8, 16 or 2n = 16, 32, 64). ‘Dili-red’ showed the highest frequency of somatic organogenesis. Fifty-nine directly regenerated plants and 293 callus-derived plants were obtained from somatic organogenesis from the cultured flowers. Based on the chromosome number, frequencies of somaclonal variation were high both in the directly regenerated plants and the callus-derived plants. The frequency of tetraploid plants (2n = 32) in the former (50%) was higher than in the latter (33%). From these results we conclude that unpollinated flower culture is an effective method for chromosome doubling simultaneously with haploid induction in shallot.