Purpose To better understand diagnostic delay and doctor-patient communication during the diagnosis of systemic lupus erythematous in patients without malar rash, we conducted a qualitative study of primary care providers’ perceptions. Methods We conducted in-depth interviews with a purposive sample of eight primary care physicians in Kaiser Permanente Northern California. Telephone interviews were recorded, transcribed, reviewed, and coded for domains and themes. Results We identified five domains related to diagnosis: initial assessment and tests, initial diagnosis and empiric treatment, timeliness of diagnosis, communicating with the patient, and opportunities for improvement. In the absence of malar rash, the lupus manifestations are common while the disease is rare. Once the primary care provider believes that the disease may be autoimmune, they work with a rheumatologist, but this could take months. Initially, the physician assesses whether the condition is self-limiting or responds to empiric treatments. Over time, as empiric treatments fail or additional lupus manifestations emerge, the primary care provider makes a referral. Doctor-patient communication is critical to help the physician make sense of the symptoms, maintain trust, and assure the patient that he or she is receiving appropriate care. Patient persistence and communication are critically important. Continuing education was deemed essential by each physician. Conclusion In the absence of malar rash, a lupus diagnosis can be difficult. Enhanced doctor-patient communication, patient persistence, physician access to rheumatology and continuing education of primary care might improve time to diagnosis and the patient’s experience with primary care. This knowledge is transferable to other rare, complex diseases.