Professional Driver Background Check Efficiency Act of 2006 - Amends federal transportation law to revise background records check requirements with respect to the issuance of a motor vehicle license for the transportation of hazardous materials to: (1) impose a fee of not more than $50 upon the applicant to cover the costs of the background check; and (2) authorize the costs for such background checks be reimbursed to the state. Prohibits an applicant from being subjected to an additional background records check or having to pay a fee in connection with applying for a transportation security card.