Medicare does not pay for routine physical exams annually for patients--a sore spot for Primary Care Providers and Medicare beneficiaries alike.  They do pay for an initial Welcome to Medicare visit.  (See the Codapedia article about that topic.)

Medicare does pay for a screening pelvic and breast exam, yearly for high risk patients and every two years for low risk patients.  Bill for this service with code G0101.  Medicare also pays for obtaining a screening pap smear, using code Q0091.

G0101 is defined as: Cervical or vaginal cancer screening; pelvic and clinical breast examination

Q0091 is defined as: Screening Papanicolaou smear; obtaining, preparing and conveyance of cervical or vaginal smear to laboratory

There is a CMS  reference guide in the resource section of this article that lists all Medicare covered preventive services, with the frequency and diagnosis codes.

Use covered diagnosis codes (V76.2, V76.47, V76.49, V15.89, V72.31)
Pelvic/breast exam G0101
Requires 7 of 11 exam elements

Examination of the breast is mandatory to bill G0101
• Inspection and palpation of the breasts for lumps, tenderness, symmetry or nipple discharge
• Digital rectal exam
Pelvic exam including:
• External genitalia
• Urethral meatus
• Bladder
• Urethra
• Vagina
• Cervix
• Uterus
• Adnexa/parametria
• Anus and perineum

This service may be billed on the same date as an Evaluation and Management service (office visit, for example) but in that case, use modifier 25 on the office visit.  Link the diagnosis codes appropriately: screening for the G0101 and the medical condition for the office visit.

Q0091 is for obtaining a screening not a diagnostic pap smear.  There is no separate code for obtaining a diagnostic pap smear.  99000, obtaining a lab specimen, is bundled by Medicare and rarely paid by other payers.