Eli Lilly's third-quarter profit surged 38 percent to $1.3 billion compared with the year-ago

period when the drugmaker recorded costs of $549.8 million for charges related to the sale of a manufacturing site and legal costs associated with Zyprexa litigation, the company announced Thursday.

The earnings figure beat analysts' estimates, although sales came in just shy of analysts forecasts at $5.7 billion, marking a 2-percent increase.

CEO John Lechleiter noted during the third quarter, international sales performed well, with revenue from Japan increasing by 27 percent "driven by recent product launches," and continued growth in "key emerging market countries, including China." The drugmaker said that healthcare reform in the US had been expected to reduce sales by approximately $65 million in the quarter, although this figure was reduced by around $25 million.

Sales of Zyprexa fell 1 percent to $1.2 billion during the period, and revenue from Cymbalta grew 4 percent to $825 million compared to the similar quarter last year.

Quarterly sales of Alimta jumped 21 percent to $560 million, which Eli Lilly said was due to increased demand and higher prices in the US, as well as "continued strong growth of the non-small-cell lung cancer indication in Japan."

In other drug sales, revenue from Humalog fell 1 percent to $494 million, while sales of Cialis rose 2 percent to $407 million. Sales of Gemzar dropped 2 percent to $325 million, as revenue from the drug continued to fall outside of the US due to generic competition in most major markets.

Lechleiter noted that "based upon our strong worldwide year-to-date results and lower estimates of the impact of US healthcare reform," the company again raised its earnings guidance for the year. Eli Lilly now forecasts earnings in the range of $4.65 to $4.75 per share, from an earlier estimate of $4.50 to $4.65 per share.

The CEO said the company was "disappointed by recent pipeline setbacks," which include the FDA's rejection of Bydureon and the failure of a late-stage trial for an experimental type 1 diabetes drug.

"They’ll get a lot of questions on their strategy for continuing to pursue the pipeline but not moving particularly aggressively" on acquisitions and partnership deals, commented Leerink Swann analyst Seamus Fernandez, who added that the delay in the approval of Bydureon could cost the company as much as $425 million in revenue.

"Overall, a reasonable quarter for the company, yet for many investors, it is the longer-term financial outlook that matters more and here, Lilly still looks challenged," commented Sanford Bernstein analyst Tim Anderson.