Women with substance use disorders (SUD) who died by suicide comprise a high-risk group of individuals in which comprehensive identification of risk factors is urgently needed to reduce rising mortality rates. Substance abuse, regardless of its type, is a significant risk factor for suicidal behavior. Overall, women with co-occurring SUD and suicidal thoughts and behavior remain a highly stigmatized and understudied group. Here we use the unique resources available in the Utah Suicide Mortality Risk Study (USMRS) to identify clinical risk factors that differentiate between women that died by suicide with SUD diagnoses and population-based control individuals (living at the time of suicide death) who also had SUD diagnoses. Diagnostic data (ICD 9&10 codes) from electronic health records (EHR) were compared between female suicide deaths at least 18 years old with SUD diagnoses (N=872; mean age = 41.5) and female controls at least 18 years old with SUD diagnoses (N=1,031; mean age = 42.0). Diagnostic data was aggregated into PheWAS trait codes (phecodes). Phecodes represent a validated way to define common conditions found in adults using EHR data. SUD diagnoses were defined by the presence of at least one diagnostic code in the “Substance addiction and disorders” phecode, encompassing diagnoses related to opioid, hallucinogen, sedative, stimulant, inhalant, cannabis, and psychoactive substance abuse. Most women with SUD diagnoses who died by suicide (~80%) had evidence of polysubstance abuse when considering the addition of complimentary data available in the USMRS. 423 phecodes, related to common medical conditions in women (>2% prevalence in suicide deaths and controls), were compared between the two groups using multivariable logistic regression models accounting for age, with FDR correction for 423 tests. 66 phecodes related to endometriosis, insomnia, irritable bowel syndrome, epilepsy, muscle spasms in addition to psychiatric diagnoses (mood disorders, anxiety disorders, personality disorders, PTSD, ADHD, schizophrenia) and diagnoses related to previous overdoses or suicide attempts were statistically more prevalent in female suicides with SUD compared to female SUD controls. 29 phecodes were statistically overrepresented in female SUD controls that involved diagnoses related to abnormal mammograms, bariatric surgery, diverticulosis, knee pain, dental pain, hypertension in pregnancy and mental disorders after pregnancy.