Walgreens Boots Alliance (WBA - Get Report) shares slid Wednesday morning despite better-than-expected earnings and a small guidance increase for 2016 as well as an assurance that the company would complete its acquisition of Rite Aid (RAD - Get Report) by the end of 2016.

Walgreens, which has a market cap of $87.38 billion, was trading at $80.93 per share Wednesday morning following earnings, down $2.59 or 3.1% from market's open.

"Shares of WBA are trading down, we believe largely due to the tax disclosure that was provided on the call," analyst David Larsen of Leerink Partners wrote in a note Wednesday. "However, we are still positive on WBA and we believe that once the deal with RAD closes, shares will likely rally."

The company reported EPS of $1.18, 4 cents more than the $1.14 EPS consensus estimate. Revenues were reported to be $29.5 billion, about $200 million less than the $29.7 consensus estimate.

As a part of its earnings, Walgreens boosted the low end of its guidance for 2016 by 10 cents per share to $4.55.

"While we continue to analyze F3Q results, we believe that F3Q:16 results are solid," Larsen wrote in a note. Larsen has an outperform rating on the company and a $95 per share price target.

Walgreens also used its earnings call to reassure investors that its acquisition of Rite Aid will close by the end of 2016.

"We are operating on the hypothesis that we will do the deal," CEO Stefano Pessina said during the company's earnings call Wednesday, reiterating the fact that the deal is expected to close by December.

According to Pessina, the company has a large team in place to work through the kinks of integrating the two stores.

He added that the company expects to have approximately 500 Rite Aid stores once the deal is closed. Walgreens will have to divest at least some Rite Aid stores thanks to antitrust regulations. For these stores, Pessina said the company is still "trying to find the right buyer."

"[The timing of the deal] doesn't depend on us," Pessina said. "The FTC will let us know when they are ready."

Walgreens also indicated that AmericansourceBergen (ABC - Get Report) will be their main source for pharmaceutical product distribution following the deal.
 
"While this seems to indicate that AmericanSource could be used for Rite Aid volumes, once the deal closes, Walgreens management stated that the decision on whether or not to use McKesson (MCK - Get Report) or AmericanSource will be made at some point in the future and relationships with both management teams are good."

As for the Brexit's effect on the company, which does about 10% of its business in the United Kingdom, Walgreens gave no indication of the Brexit's impact on its earnings in its SEC filings, but said during its earnings call that it is too soon to tell.

"I believe that once the emotional part is gone, things will settle down," said George Fairweather, Walgreens executive vice president and CFO. "We will have an idea of what is happening."

However, the company noted that "people still buy beauty in tough times" and expects its business to remain relatively strong in the U.K. despite its vote to leave the European Union.

In the United States, though, Walgreens' retail business could continue to carry the company's weight.

"In our view earnings in retail USA are solid and somewhat of a relief given the fact that the new Medicare Part D rates went into effect 1/1/16 and this quarter reflects the full impact of that incremental volume," Larsen wrote.

Walgreens could not be reached for immediate comment following earnings.

Rite Aid's shares spiked slightly on the news, trading at $7.40 per share Wednesday morning, up 1.37% from market's open.

Jim Cramer and Research Director Jack Mohr wrote that these results are "a solid beat and raise." Walgreens is a holding in Jim Cramer's Action Alerts PLUS Charitable Trust Portfolio. Want to be alerted before Cramer buys or sells WBA? Learn more now.

"We view the results as solid yet neutral, and are more interested in management's commentary" on a Wednesday morning conference call, Cramer and Mohr added.

This article was updated to reflect midday share price and additional analyst commentary.