Third-quarter profit at Eli Lilly and Co. missed analysts' estimates, and the Indianapolis-based drugmaker lowered its profit forecast by 4 cents per share for the remainder of the year.

Shares in Lilly were down more than 2 percent at midday Wednesday, to $50.76 each.

Lilly earned $1.3 billion during the three months ended Sept. 30, up by 7 percent from the same period a year ago. But that boost was due largely to an early payoff from former drug-development partner Amylin Pharmaceuticals Inc.

Excluding the Amylin payments and other special items, Lilly’s profit would have fallen to $888 million, a whopping 29-percent decline from the same period last year. On that basis, earnings per share were 79 cents in the most recent quarter.

Wall Street analysts were expecting 83 cents per share, according to a survey by Thomson Reuters.

Lilly’s revenue also was below analysts’ forecasts. The company brought in $5.44 billion during the quarter, down 11 percent from the same quarter last year. Analysts were expecting $5.62 billion.

Lilly lowered its full-year profit forecast to a range of $3.68 per share to $3.78 per share. Larger asset impairment and restructuring costs shaved 4 cents from the forecast issued in August.

However, excluding all special gains or losses, Lilly still expects to earn from $3.30 per share to $3.40 per share, the same as it had forecast in August.

“Lilly reported a ho-hum quarter,” Mark Schoenebaum, an analyst with ISI Group in New York, said in a note to clients, according to Bloomberg News. “Marginally weak financial quarter, but nothing terrible.”

Lilly’s revenue has been falling because its former bestseller Zyprexa lost patent protection a year ago. Lilly has been trying to offset the loss of $2.5 billion in Zyprexa revenue so far this year by improving sales of other drugs.

In the third quarter, sales of the antidepressant Cymbalta, the osteoporosis drug Forteo and Lilly’s animal health products all grew 20 percent or more over the same quarter last year.

Lilly also received $1.26 billion from Amylin following Amylin's acquisition by New York-based Bristol-Myers Squibb Co. Lilly and Amylin had co-developed the diabetes drugs Byetta and Bydureon. But a dispute last year led to a break-up of their partnership.

Lilly’s shares fell Tuesday prior to the earnings announcement by less than 1 percentage point, to $51.91. The stock had been flat all year until Aug. 24, when Lilly announced its experimental Alzheiemer’s drug solanezumab had shown some positive effects on patients. Since then, Lilly’s shares have traded up 22 percent.