BACKGROUND: Preparing for natural disasters has historically focused on treatment for acute injuries, environmental exposures, and infectious diseases. Many disaster survivors also have existing chronic illness, which may be worsened by post-disaster conditions. The relationship between actual medication demands and medical relief pharmaceutical supplies was assessed in a population of 18,000 evacuees relocated to San Antonio TX after Hurricane Katrina struck the Gulf Coast in August 2005. METHODS: Healthcare encounters from day 4 to day 31 after landfall were monitored using a syndromic surveillance system based on patient chief complaint. Medication-dispensing records were collected from federal disaster relief teams and local retail pharmacies serving evacuees. Medications dispensed to evacuees during this period were quantified into defined daily doses and classified as acute or chronic, based on their primary indications. RESULTS: Of 4,229 categorized healthcare encounters, 634 (15%) were for care of chronic medical conditions. Sixty-eight percent of all medications dispensed to evacuees were for treatment of chronic diseases. Cardiovascular medications (39%) were most commonly dispensed to evacuees. Thirty-eight percent of medication doses dispensed by federal relief teams were for chronic care, compared to 73% of doses dispensed by retail pharmacies. Federal disaster relief teams supplied 9% of all chronic care medicines dispensed. CONCLUSIONS: A substantial demand for drugs used to treat chronic medical conditions was identified among San Antonio evacuees, as was a reliance on retail pharmacy supplies to meet this demand. Medical relief pharmacy supplies did not consistently reflect the actual demands of evacuees.