Abstract Study question Do differences in the morphological characteristics of embryos or the dynamics of the developmental process affect the results of niPGT analysis? Summary answer Embryos with blastomeres that were excluded at compaction showed reduced accuracy of niPGT analysis, but other measured morphological characteristics had no impact. What is known already The PGT-A test, is invasive and requires training to be competent at the technique, aswell as the need for specialized equipment and consumables. In recent years, non-invasive PGT-A (niPGT-A), which analyzes Cell-Free DNA released from cultured embryos, has been attracting attention. Regarding the analysis accuracy of niPGT-A, there are reports that it is equivalent to or even superior to conventional PGT-A. However, at present, it is not clear how methodological differences or embryo dynamics impact results. Study design, size, duration From August 2021 to February 2022, 284 pronuclear-stage frozen embryos (with consent for research use), were thawed and cultured. They were individually cultured for at least 40 hours after Day 4. For the 150 embryos that reached the blastocyst stage, culture medium and the blastocysts were collected and subjected to chromosome aneuploidy analysis by NGS. For the 138 blastocyst with a result, the concordance rate was calculated with that obtained from the culture medium samples. Participants/materials, setting, methods The embryos were individually cultured in a single step medium using a 10 μl droplet from Day 4. The entire culture period was recorded in a time-lapse incubator. The concordance rate for all chromosomes between culture medium sample and the blastocyst was compared to recorded embryo dynamics, e.g. presence or absence of cumulus cell attachment, sperm attachment, fragmentation, blastomeres that excluded at compaction, shrinkage, and hatching. Chi-square test was used to compare the concordance rates. Main results and the role of chance The overall concordance rate for all chromosomes between the culture medium and the blastocysts samples was 46.4%(64/138). In the blastocysts where there were cumulus cells attached or not it was 43.6% (17/39) vs 47.5% (47/99) respectively, cases where there was still a sperm attached or not it was 53.1% (17/32) vs 44.3% (47/106) resepctively and in blastocysts where there had been fragmentation or no fragmenattion it was 46.9%(38/81) vs 45.6%(26/57) respectively. In cases where shrinkage of the blastocyst had been observed vs no shrinkage the respective concordance rates were 44.9% (48/107) vs 51.6% (16/31), whilst in cases where the blastocyst had hatched or not it was 40.6% (13/32) vs 48.1% (51/106) respectively.For the blastocysts where the blastomeres had been excluded at compaction or not it was 35.6%(31/87) vs 64.7% (33/51) respectively.Significant differences were only identified in cases with blastomere exclusion or no exclusion at compaction (P < 0.01). Limitations, reasons for caution In this study, the culture was continued to day 6 regardless of morphology of the embryo on day 5, which differs from the usual clinical culture process. Wider implications of the findings These results are useful in that they may aid in recognising which morphological features of embryos may impact the results obtained from niPGT and hence its reliability for clinical application. The blastomeres that excluded at compaction are clearly important for improving the accuracy of the niPGT analysis in the future. Trial registration number None