BREEDPLAN, the Australian beef cattle genetic evaluation system, uses ultrasound scan intramuscular fat as a correlated trait for predicting carcase intramuscular fat. More recently, it has been observed that seedstock herds are being scanned at younger ages and lower levels of fatness and this research was undertaken to examine the effect on heritability and the genetic correlation estimates when scan records are removed using fat depth thresholds. Using BREEDPLAN data to estimate these genetic relationships, this study yielded genetic correlation estimates of 0.37 and 0.36 in Angus and 0.69 and 0.54 in Hereford for bull and heifer scan intramuscular fat, respectively. The results showed a useful improvement in the genetic correlation between bull intramuscular fat and carcase intramuscular fat in Angus cattle to 0.48. However, for Angus heifers and Hereford bulls and heifers there was no significant improvement, suggesting that strategies to reduce lean scanning will not improve the genetic correlation estimates in those cases.