Updated from 5:01 p.m. EDT

Excluding Tysabri expenses and merger-related costs,

Biogen Idec

(BIIB) - Get Report

beat Wall Street's earnings estimates for the latest quarter and reported better-than-expected sales of its top two drugs.

The Cambridge, Mass., biotech company said Tuesday it earned $35 million, or 10 cents a share, in the second quarter.

Before a charge of $20 million, or 4 cents a share, from Tysabri inventories written off during the quarter, merger-related accounting expenses of $86 million, and $78 million in charges related to the sale of a manufacturing facility, earnings were $149 million, or 43 cents a share. Analysts expected a profit of 36 cents a share.

During the first quarter, Biogen pulled its multiple sclerosis drug Tysabri from the market after cases of a rare brain disease were linked to its use. The company recorded charges of about $36 million from the withdrawal in that quarter.

Thanks to sales of Avonex, which is also for multiple sclerosis, and Rituxan for B-cell non-Hodgkin's lymphoma, Biogen's revenue rose 12% to $606 million from $539 million last year. The consensus estimate was $599.3 million for the quarter.

Avonex, now the leading MS drug worldwide, brought in sales of $382 million, up 10% from a year earlier, and Rituxan revenue totaled $185 million, up 22%. Biogen co-promotes Rituxan with

Genentech

(DNA)

.

"Impressive results from Avonex and Rituxan, coupled with operational discipline and effective cost management, drove an increase of more than 20% in earnings," said James Mullen, Biogen Idec's chief executive, in a press release. "We have also maintained our strong commitment to the MS community by conducting an extensive safety evaluation of Tysabri which is ongoing. We look forward to the expected completion of the evaluation by the end of the summer and to further discussions with the regulatory authorities regarding the path forward for Tysabri."

During its conference call, Biogen declined to issue guidance for the year. The company also wouldn't comment on the number of PML cases discovered in Tysabri users or the results of safety evaluations of the drug. The company did say that the evaluations are going well and that it expects the drug to return to the market.

Shares of Biogen were down 38 cents to $38.44 after hours Tuesday.