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To evaluate the outcome of 342 pregnancies reported antenatally with short long bones (SLBs) or IUGR to the East Midlands and South Yorkshire Congenital Anomaly Register (EMSYCAR) over a five year period (2008–2012).SLBs and IUGR are ‘soft’ markers identified during pregnancy with potentially serious outcomes of skeletal and chromosomal abnormalities. The extent of the overlap between the two markers is unclear.Between 2008 and 2012, 377,652 births were monitored by EMSYCAR. All anomalies reported in pregnancies within the region were coded to ICD-10; all soft markers were coded according to a protocol agreed by the British Isles Network of Congenital Anomaly Registers.227 cases were identified antenatally with SLBs (6.01/10,000) and 115 cases with IUGR (3.05/10,000) including 13 cases that reported both. 32 (14.1%) of the SLBs cases had a chromosomal anomaly, 75 (33.0%) an isolated skeletal anomaly, 21 (9.2%) a serious non-skeletal anomaly, 41 (18.1%) had both and 58 (25.6%) completely resolved. 20 (17.4%) of the IUGR cases had a chromosomal anomaly, 19 (16.5%) an isolated skeletal anomaly, 36 (31.3%) a serious non-skeletal anomaly, 24 (20.9%) had both and 16 (13.9%) fully resolved.An antenatal diagnosis of SLBs appears more indicative of an isolated skeletal anomaly than IUGR; the reverse is true for non-skeletal anomalies. Although SLBs are more widely reported antenatally, the proportion that resolved before delivery (25.6% C. I. 20.0; 31.7) is almost twice that of IUGR cases (13.9% C. I. 8.1; 21.6), strongly suggesting the latter indicates a poorer overall prognosis at birth.