Background This study investigates possible changes in the frequency of trinucleotide repeat dynamic mutations in offspring conceived through assisted reproductive technology (ART) in comparison with matched controls from spontaneous pregnancies.Methods A prospective clinical observational study was performed on two hundred and forty-six families recruited from the in vitro fertilisation centre at a tertiary-care, university-affiliated, teaching hospital.Parental, peripheral and umbilical cord blood samples were collected and the trinucleotide repeat dynamic mutation genes of ATN1, AR, ATXN1, ATXN3, Huntington, DMPK and FMR-1 were investigated between generations.The frequencies and sizes of the mutational repeats of intergenerational instability were measured.Results A total of 2,466 transmissions were identified in ART offspring, with 2.11% (n=52/2,466) of alleles being unstable upon transmission.In the control group, the frequency of dynamic mutation was 0.77% (n=10/1,300).Stati <0.01).The unstable transmission alleles were detected in 32 (2.48%) of 1,288 alleles in in vitro fertilisation (IVF) offspring and 20 (1.70%) of 1,178 alleles in intracytoplasmic sperm injection (ICSI) offspring, which were significantly different from naturally conceived babies (0.77%, 10/1,300) (P<0.01 and P<0.05, respectively).However, there were no significant differences in the size of mutational repeats, the rates of expansion or the rates of contraction among the three groups (P>0.05).The repeat copy numbers of examined genes in all parents and their babies were found to be within the normal ranges.Conclusions Our results illustrated that more significant alterations in the frequency of trinucleotide repeat dynamic mutations in offspring conceived through ART.Additional studies determining the factors that influence instability of genome in ART procedure are urgently needed.