Border Improvement and Immigration Act of 1999 - Amends the Illegal Immigration Reform and Immigrant Responsibility Act of 1996 with respect to the automated entry-exit control system to exempt from required recordkeeping: (1) land border crossings and seaports; and (2) permanent resident and certain other aliens.

(Sec. 3) Requires the Attorney General to report: (1) on the feasibility of implementing an automated entry-exit control system that would include land border and seaport arrivals and departures; and (2) annually on the development status of the automated entry-exit control system, and on visa overstays identified through such system. Requires integration of overstay information into Department of State and Immigration and Naturalization Service (INS) databases.

(Sec. 5) Authorizes appropriations for INS and United States Customs Service border control and enforcement activities. Sets forth specified set-asides. Authorizes: (1) use of equipment funds for new technologies; and (2) transfer up to ten percent of specified set-asides for other equipment uses. Sets aside specified funds for peak hours and investigative resource enhancement.

Provides for increased numbers of full-time INS and Customs inspectors at U.S. land borders.