Abstract Motivation Meiotic recombination is the main driving force of human genetic diversity, along with mutations. Recombinations split into crossovers, separating large chromosomal regions originating from different homologous chromosomes, and non-crossovers (NCOs), where a small segment from one chromosome is embedded in a region originating from the homologous chromosome. NCOs are much less studied than mutations and crossovers as NCOs are short and can only be detected at markers heterozygous in the transmitting parent, leaving most of them undetectable. Results The detectable NCOs, known as gene conversions, hide information about NCOs, including their number and length, waiting to be unveiled. We introduce NCOurd, software, and algorithm, based on an expectation–maximization algorithm, to estimate the number of NCOs and their length distribution from gene conversion data. Availability and implementation https://github.com/DecodeGenetics/NCOurd