Koubek turned professional in 1994, between 1994 and 1998, Koubek mostly played in ATP Futures and ATP Challenger Series events. In 1997 he jumped up 184 positions in the rankings, thanks to good results in Challenger tournaments, reaching finals in Ulm and Alpirsbach. 1998 saw Koubek win his first Challenger event in Alpirsbach; later that same year he lost to Younes El Aynaoui in the final of Maia. Koubek compiled a 33-20 record for the year.
Koubek won his first ATP title in 1999 at Atlanta as a qualifier. He achieved this losing only one set in the whole tournament, overcoming Sébastien Grosjean in the final 6–1 6–2.
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