Health Insurance Affordability and Equity Act of 1999 - Amends the Internal Revenue Code to allow as a tax credit an amount equal to 60 percent of the amount paid (not to exceed the sum of the monthly limitations for eligible months) for qualified health insurance coverage for the taxpayer, the taxpayer's spouse, and dependents. Define "eligible month" as any month which begins at least one year after the most recent month that the individual was eligible to participate in any group health plan of an employer which provided qualified health insurance or participated in any group health plan of any other entity which provided such insurance.

Allows as a deduction an amount equal to the applicable percentage of the amount paid for qualified health insurance coverage for a taxpayer, his spouse, and dependents. Increases, incrementally, the percentage from 60 percent in calendar year 2000 to 100 percent for calendar years 2004 and thereafter. Excludes coverage under which less than 50 percent of the cost of coverage is borne by the taxpayer.