The pygmy bluetongue lizard, Tiliqua adelaidensis, is an endangered scincid lizard that occurs in remnants of natural grasslands in the mid-north of South Australia. We assessed the factors affecting body condition of male and female lizards, using body size residuals as an index, over five sampling years. We included sex, phenotypic (patterned or plain morphs), temporal (sampling year and activity period within year), and climatic factors in our analyses. The results indicated that sampling year and activity period within the year were the two most important factors influencing variation in body condition of both male and female lizards over the period of the study. There were similar trends when we considered males and females separately. However, when prepartum and postpartum females were analysed separately, sampling year did not affect their body condition. None of the analyses showed any significant effect of phenotype on body condition. Winter–spring rainfall was positively correlated with body condition of females in the prepartum period, but showed no significant effect on mean body condition of any other grouping of adult lizards, nor a consistent direction of correlation among the different subsets of adult lizards that we considered. The substantial annual variations in the body condition of lizards, although of uncertain cause, provide important information for conservation managers who monitor persisting populations of this endangered species.