Health Savings and Affordability Act of 2009 - Amends the Internal Revenue Code to: (1) allow a tax deduction from gross income for the cost of health insurance coverage for individual taxpayers, their spouses, and dependents; (2) permit holders of health savings accounts (HSAs) and their spouses who are age 55 or older to make additional (catch-up) contributions to a joint HSA; (3) increase the allowable amount of the tax deduction for contributions to HSAs; (4) combine individual and family deductibles under high deductible health insurance plans; (5) allow for increased rollovers from flexible spending arrangements (FSAs) or health reimbursement arrangements (HRAs) into HSAs; (6) allow the payment of premiums from HSAs for high deductible health plans; and (7) treat as medical care for purposes of the tax deduction for medical expenses certain exercise equipment and fees for physical fitness programs.