2006 was a breakthrough year for Bondarenko as she made it inside the top 50, after quarterfinal appearances at Hobart and Bangalore, and first-round exits in Pattaya and at the Australian Open as well as early exits in Dubai, Doha, and Indian Wells. With her early exit in Indian Wells, Bondarenko decided to compete in Orange in California an ITF event claiming the title over Yvonne Meusburger 6–3, 7–5. Then she made stellar performances in the WTA Tour, making it to the third round of the Pacific Life Open entering as a qualifier, losing to Ana Ivanovic 3–6, 7–5, 3–6.