Working Uninsured Tax Equity Act of 1999 - Amends the Internal Revenue Code to allow an individual a refundable tax credit equal to 30 percent of the amount paid during the taxable year for insurance which constitutes medical care for the taxpayer, the taxpayer's spouse, and dependents. Disallows such a credit for: (1) any taxpayer eligible to participate in his or her employer's (or spouse's employer's) subsidized health plan; or (2) Medicare or Medicare supplemental policy payments.

Limits the full credit to individuals whose adjusted gross income is under $30,000 ($50,000 if filing a joint return). Disallows any credit to a married individual filing a separate return, but treats married individuals living apart and filing separate returns as not married (thus qualifying them for the credit). Prescribes a formula for phase-out of the credit for taxpayers with an adjusted gross income exceeding $30,000 ($50,000 for a joint return) by less than $10,000.

Allows self-employed individuals to elect such credit or the deduction for medical expenses, but not both.

States that such credit does not apply to long- term health care insurance.