This report briefly describes the content and objective of the Department of Energy civilian and defense R&D programs, the FY1999 budget request for each of those programs, and congressional appropriations and authorization actions. It then discusses several issues that emerged during congressional consideration of the DOE budget including the Climate Change Technology Initiative, the nuclear energy research initiative, the fusion energy sciences program, the spallation neutron source, and the stockpile stewardship program, and how those issues were dealt with by Congress for FY1999. This report should provide an useful overview of the DOE R&D programs, their FY1999 appropriations andauthorization history, and the potential implications of those actions. The current version of this report is the final one for 1998. A new report will be prepared for the FY2000 budget cycle.