Objective To investigate differences in risk factors for depression and anxiety, such as central nervous system involvement in systemic lupus erythematosus (SLE)/mixed connective tissue disease (MCTD), by comparing youth with SLE/MCTD to peers with type 1 diabetes mellitus (T1D). Study design We conducted a cross-sectional study of 50 outpatient pairs, ages 8 years and above, matching subjects with SLE/MCTD and T1D by sex and age group. We screened for depression, suicidal ideation, and anxiety using the Patient Health Questionnaire-9 and the Screen for Childhood Anxiety Related Emotional Disorders, respectively. We collected parent-reported mental health treatment data. We compared prevalence and treatment rates between subjects with SLE/MCTD and T1D, and identified disease-specific risk factors using logistic regression. Results Depression symptoms were present in 23%, suicidal ideation in 15%, and anxiety in 27% of participants. Compared with subjects with T1D, subjects with SLE/MCTD had lower adjusted rates of depression and suicidal ideation, yet poorer rates of mental health treatment (24% vs 53%). Non-White race/ethnicity and longer disease duration were independent risk factors for depression and suicidal ideation. Depression was associated with poor disease control in both groups, and anxiety with insulin pump use in subjects with T1D. Conclusion Depression and anxiety are high and undertreated in youth with SLE/MCTD and T1D. Focusing on risk factors such as race/ethnicity and disease duration may improve their mental health care. Further study of central nervous system and other disease-related factors may identify targets for intervention.