An Australian food composition database, AUSNUT1999, does not include long chain omega-3 polyunsaturated fatty acid (LC omega-3 PUFA) data. Measurement of the fatty acid content of diets initially analysed using AUSNUT1999 requires conversion to AUSNUT2007, an updated database inclusive of LC omega-3 PUFA. The aim of this study was to convert clinical trial dietary data from AUSNUT1999 to AUSNUT2007 and measure LC omega-3 PUFA intake. Clinical trial diet history (DH) data was converted from AUSNUT1999 to 2007 using a staged approach. Macronutrient intake from AUSNUT1999 and 2007 were calculated and compared via paired t-tests and Wilcoxon Signed Ranks tests. Mean dietary LC omega-3 PUFA intake and the percentage contribution of food groups to total LC omega-3 PUFA were then calculated. DHs were collected at baseline (n = 118), three months (n = 86), and 12 months (n = 64). The accuracy of the conversion process improved with time, with no significant difference between most macronutrients at 12 months. Mean LC n-3 PUFA intake was 441.87 mg at baseline, 521.07 mg at 3 months, and 442.40 mg at 12 months, and was predominantly provided by fish and seafood, followed by meat products. This study allowed for the measurement of LC omega-3 intake, which was previously impossible using the AUSNUT1999 database.