Nano-exons are exons less than 4 nt. long. Because nano-exons are so small, they often go undetected, and the number of nano-exons remains unknown. We have examined a single high-quality RNA-seq data set in depth using a bioinformatics pipeline to discover and quantify nano-exons. These data are derived from Drosophila hemocytes, both wild-type and expressing an A2bp1 RNAi transgene. A2bp1 is a member of the highly conserved Fox-1 family of RNA-binding proteins. Human homologs RBFOX1, RBFOX2 and RBFOX3 have been linked to brain development, cardiac function, and autism spectrum disorders, and have been implicated in the regulation of microexons less than 51 nt. in humans. Our analysis has revealed new potential nano-exons in Drosophila, including eight previously undescribed nano-exons with strong support. We also found three likely cases of recursive splicing with deletion that can be considered to be exons of size -1, meaning that sequences within an intron, including the sequence AGT, result in the removal of one nucleotide due to recursive splicing. Each of these three cases (in Rpl8, orb and Axn) occurs within highly conserved 5' UTR sequences, but their regulatory significance remains unknown. Ongoing research explores the occurrence of nano-exons in other Drosophila data sets and in other species.