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We examined associations between dietary patterns at 12 months, characterised using multiple methodologies, and risk of obesity and early childhood caries (ECC) at 24&#8722;36 months. Participants were Australian toddlers (n = 1170) from the Study of Mothers&#8217; and Infants&#8217; Life Events affecting oral health (SMILE) birth cohort. Principal Components Analysis (PCA) and the Dietary Guideline Index for Children and Adolescents (DGI-CA) were applied to dietary intake data (1, 2 or 3-days) at 12 months, and regression analysis used to examine associations of dietary patterns with body mass index <i>Z</i>-score and presence of ECC at 24&#8722;36 months. Two dietary patterns were extracted using PCA: <i>family diet</i> and <i>cow&#8217;s milk</i> <i>and</i> <i>discretionary combination</i>. The mean DGI-CA score was 56 &#177; 13 (out of a possible 100). No statistically significant or clinically meaningful associations were found between dietary pattern or DGI-CA scores, and BMI <i>Z</i>-scores or ECC (n = 680). Higher <i>cow&#8217;s milk and discretionary combination</i> pattern scores were associated with higher energy and free sugars intakes, and higher <i>family diet</i> pattern scores and DGI-CA scores with lower free sugars intakes. The association between dietary patterns and intermediate outcomes of free sugars and energy intakes suggests that obesity and/or ECC may not yet have manifested, and thus longitudinal investigation beyond two years of age is warranted.